Escherichia coli is a normal parasitic bacterium in the intestinal tract and is an important indicator of the degree of contamination and hygienic quality of water bodies. In this study, 78 samples of domestic drinking water were tested for Escherichia coli by filter membrane method and multi-tube fermentation method. The results showed that the passing rate of water samples tested by the multi-tube fermentation method was higher than that of the filter membrane method, which was statistically significant (P < 0.05). In the untreated water samples test, the detection rate of Escherichia coli was 92.31% in the multi-tube fermentation method compared to 71.79% in the filter membrane method, and the difference was statistically significant. The results of the study showed that the detection rate and sensitivity of the multi-tube fermentation method in the microbiological testing of domestic drinking water were higher and better than that of the filter membrane method. The selection of testing methods should consider its applicability and the accuracy of the test results. Meanwhile, factors affecting the quality of microbiological testing include the quality of laboratory personnel, specimen handling, and the quality of instruments and reagents, which need to be carefully managed and trained. This study can provide a practical reference for microbiological testing of domestic drinking water.